phylogeography phylogenetics ounderstanding phylogenetic trees omajor approaches to determining...
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Phylogeography
Phylogenetics
o Understanding phylogenetic trees
o Major approaches to determining phylogenies
Phylogeography
Phylogenetics Study of the evolutionary relationships among
individuals, groups, or species
Relationships often represented as dichotomous branching tree
Extremely common approach for detecting and displaying relationships among genotypes
Important in evolution, systematics, and ecology (phylogeography)
A
B M
K
IJ
N
L
H
G
F
E
D
C
ZYXWVUT
PQ
SR
O
Ç
Evolution
What is a phylogeny?
ZYXWVUT
PQ
SR
O
Ç Homology: similarity that is the result of inheritance from a common ancestor
Phylogenetic Tree Terms
A B C D E F G H I J
ROOT
interior branches
node
terminal branches
Leaves, Operational Taxonomic Units (OTUs)
Group, cluster, clade
Bacteria 1
Bacteria 3
Bacteria 2
Eukaryote 1
Eukaryote 4
Eukaryote 3
Eukaryote 2
Tree Topology
(Bacteria1,(Bacteria2,Bacteria3),(Eukaryote1,((Eukaryote2,Eukaryote3),Eukaryote4)))
Bacteria 1
Bacteria 3Bacteria 2
Eukaryote 1
Eukaryote 4Eukaryote 3
Eukaryote 2
http://helix.biology.mcmaster.ca
How about these?
Are these trees different?
Rooted versus Unrooted Trees
archaea
archaea
archaea
eukaryote
eukaryote
eukaryote
eukaryote
Unrooted tree
Rooted by outgroup
bacteria outgroup
root
eukaryote
eukaryote
eukaryote
eukaryote
archaea
archaea
archaea
Monophyletic group
Monophyleticgroup
D
C
B
AG
E
F
C
B
A
F
E
G
D
Rooting with D as outgroup
D
C
B
AG
E
F
C
B
A
F
E
G
D
C
B
A
F
E
G
D
Now with C as outgroup
Which of these four trees is different?
Baum et al.
Phenetics (distance) vs Cladistics (character state
based) Lowe, Harris, and Ashton 2004
Choosing Phylogenetic Trees MANY possible trees can
be built for a given set of taxa
Very computationally intensive to choose among these
Lowe, Harris, and Ashton 2004
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)!52(3
n
nU
nN nnN Unn
nR )32(
)!2(2
)!32(2
7
9
8
9
9
9
9
5
8
10
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11
Felsenstein 2004
Choosing Phylogenetic Trees Many algorithms exist for
searching tree space
Local optima are problem: need to traverse valleys to get to other peaks
Heuristic search: cut trees up systematically and reassemble
Branch and bound: search for optimal path through tree space
Phylogeography
The study of evolutionary relationships among individuals based on phylogenetic analysis of DNA sequences in geographic context
Can be used to infer evolutionary history of populations
Migrations Population subdivisions Bottlenecks/Founder Effects
Can provide insights on current relationships among populations
Connectedness of populations Effects of landscape features on gene flow
Phylogeography Topology of tree provides
clues about evolutionary and ecological history of a set of populations
Dispersal creates poor correspondence between geography and tree topology
Vicariance (division of populations preventing gene flow among subpopulations) results in neat mapping of geography onto haplotypes
Example: Pocket gophers (Geomys pinetis)
Fossorial rodent that inhabits 3-state area in the U.S.
RFLP for mtDNA of 87 individuals revealed 23 haplotypes
Parsimony network reveals geographic relationships among haplotypes
Haplotypes generally confined to single populations
Major east-west split in distribution revealed
Avise 2004
Avise 2004
I
II
III
IV
V
Example: Brown Bears (Ursus arctos) Reduced to <1%
of original range in North America
Sequence mtDNA control region of bears from worldwide distribution
Notice unique haplotype F in ABC islands of Alaska
Notice position of polar bear
Lowe, Harris, and Ashton 2004
Brown Bear Surprise Subsequent study of samples from ice cores
(36,000-43,000 years old) found all four haplotypes
How do you explain the modern distribution?
Current Ancient
Brown Bears in North America (Ursus arctos) Diversity assessed
based on 8 microsatellite loci
Reduced diversity for more isolated sites (Kodiak, Yellowstone)
Brown Bear Nuclear Differentiation Assessed differentiation based
on 17 nuclear microsatellite loci
Strong differentiation between Kodiak and Admiralty islands
Lowe, Harris, and Ashton 2004
Brown Bear Nuclear Differentiation Less differentiation for
nuclear than mitochondrial markers
Degree of differentiation driven by distances between islands: Admiralty much more divergent than Chicagof or Baranof
Why?
Lowe, Harris, and Ashton 2004
T
SST H
HG 1
SH1
Also, maternal inheritance of mitochondrion
Smaller effective population size of mitochondrion
Mitochondrion is one locus: selective sweeps!
Ursus arctos in Europe Highly degraded populations,
low genetic diversity
Haplotypes reveal 3 refugia during glaciation
Migration and admixture following deglaciation (“suture zones” in Scandinavia and central Europe)
Taberlet et al. 1998; Molecular Ecology
7:453
Human Phylogeography Most evidence points to origins in Africa and
subsequent migrations
Cavalli-Sforza 2003 Nature Genetics 33:266
Human Phylogeography: mtDNA Most ancient and diverse
haplotypes in Africa (dots)
Migration and admixture is evident from presence of African haplotypes in other clades
Human Phylogeography: X-chromosome genes Pyruvate dehydrogenase
E1 alpha subunit sequence
25 polymorphic sites, 23 of which were in African sample
African θ=6.9, non-African θ=0.57
Using chimp sequence as outgroup, estimated that divergence occurred 1.9 million years ago
Complexities to Human Phylogeography Some genes show evidence of Asian origin
Sequence of X-linked ribonucleotide reductase M2 pseudogene 4
Suggests single origin model is too simple: admixture and selection?
Garrigan 2007 Nature Reviews Genetics 7:669
Evidence of Admixture in Ancient Eurasians
Garrigan 2007 Nature Reviews Genetics 7:669
Evidence for Ancient Population Structure in Nuclear but not Mitochondrial Trees
Garrigan 2007 Nature Reviews Genetics 7:669
Evidence for Ancient Population Structure in Nuclear but not Mitochondrial Trees
Garrigan 2007 Nature Reviews Genetics 7:669
Alternative Models to Single Origin
Garrigan 2007 Nature Reviews Genetics 7:669
Human Phylogeography with SNP Assayed 500,000 SNP genotypes for 3,192 Europeans
Used Principal Components Analysis to ordinate samples in space
High correspondence betweeen sample ordination and geographic origin of samples
Individuals assigned to populations of origin with high accuracy
Nested Clade Analysis
Combines spatial and temporal tests of association
Can be used to distinguish ongoing population processes from historical events
Dc – Clade distance (measures geographic range of a particular clade)Dn – Nested clade distance (geographic relationship to other same level categories)I-T – average distance between interior and tip clades within nested group
Branco et al 2002 Evolution 56:792–803
Use random permutation testing to test significance of associations
Templeton AR 1998 Molecular Ecology 7:381-397
Nested Clade Analysis - critique and summary (reflections of a colleague)
Hardly anyone believes in it anyway (ie Wayne Maddison is strongly against it, because it is too conjectural - not statistically sound)
All you need to know is that people use it to make conclusions about range expansions and historical vicariant events, based on molecular data
The method replies on this inference key, which ultimately tells you nothing in the end